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"SAS_MAF": "G:0.1203", "SIFT": "", "SOMATIC": "", "STRAND": "1", "SWISSPROT": "", "SYMBOL": "PPARG", "SYMBOL_SOURCE": "HGNC", "TREMBL": "Q6L9M1\u0026Q4W448", "TSL": "", "UNIPARC": "UPI00005197A4", "VARIANT_CLASS": "SNV", "ancestral": "C", "cDNA_position": "", "context": "CCC", "major_consequence": "intron_variant"}], "xpos": 3012393125, "xstart": 3012393125, "xstop": 3012393125};
        window.base_coverage = [{"1": 1.0, "10": 0.9994, "100": 0.2468, "15": 0.9984, "20": 0.9961, "25": 0.9935, "30": 0.989, "5": 1.0, "50": 0.8706, "has_coverage": true, "mean": 74.32, "median": 74.0, "pos": 12393125}];
        window.any_covered = true;
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                draw_region_coverage(window.base_coverage, $(this).val(), window.variant.ref);
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    .axis path, .axis line {
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        shape-rendering: crispEdges;
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    </style>
    <script>
        var af_buckets = [0.0001, 0.0002, 0.0005, 0.001, 0.002, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.5, 1];
        function get_af_bucket_text(bin) {
            if (bin == 'singleton' || bin == 'doubleton') {
                return 'This is the site quality distribution for all ' + bin + 's in ExAC.';
            } else if (bin == '0.0001') {
                return 'This is the site quality distribution for all variants with AF < ' + bin + ' in ExAC.';
            } else {
                return 'This is the site quality distribution for all variants with ' + af_buckets[af_buckets.indexOf(parseFloat(bin)) - 1] + ' < AF < ' + bin + ' in ExAC.';
            }
        }
        $(document).ready(function() {
            $('.frequency_display_buttons').change(function() {
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                var v = $(this).attr('id').replace('_button', '');
                $('#' + v + '_container').show();
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            $('#frequency_table').tablesorter({
                stringTo: 'bottom',
                sortList: [[4,1], [0,0]],
                headers: {
                    4: {
                        sorter: 'digit'
                    }
                }
            });

            if (window.variant != null && 'genotype_depths' in window.variant) {
                draw_quality_histogram(window.variant.genotype_depths[1], '#quality_display_container', false, 'Depth', 'Variant Carriers');
                $('.quality_display_buttons').change(function() {
                    var v = $(this).attr('id').replace('_button', '');
                    var f = $('.quality_full_site_buttons.active').attr('id') == 'variant_site_button' ? 0 : 1;
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                    draw_quality_histogram(window.variant[v][f], '#quality_display_container', false, $(this).text(), ylab);
                });
                $('.quality_full_site_buttons').change(function() {
                    var v = $('.quality_display_buttons.active').attr('id').replace('_button', '');
                    var f = $(this).attr('id') == 'variant_site_button' ? 0 : 1;
                    var ylab = f ? 'Variant Carriers' : 'Individuals';
                    draw_quality_histogram(window.variant[v][f], '#quality_display_container', false, $('.quality_display_buttons.active').text(), ylab);
                });

                // Quality metric histograms
                var data = _.zip(_.map(window.metrics['Site Quality']['mids'], Math.exp), window.metrics['Site Quality']['hist']);
                draw_quality_histogram(data, '#quality_metric_container', true, 'Site Quality', 'Variants');
                var bin = window.metrics['Site Quality']['metric'].split('_')[1];
                $('#site_quality_note').html(get_af_bucket_text(bin));
                var pos = $('#quality_metric_select').val().split(': ')[1];
                add_line_to_quality_histogram(data, pos, '#quality_metric_container', true);
                var log_these = ['Site Quality', 'DP'];
                $('#quality_metric_select').change(function() {
                    var v = $(this).val().split(': ');
                    var log = false;
                    $('#site_quality_note').html('');
                    var data;
                    if (log_these.indexOf(v[0]) > -1) {
                        data = _.zip(_.map(window.metrics[v[0]]['mids'], Math.exp), window.metrics[v[0]]['hist']);
                        log = true;
                    } else {
                        data = _.zip(window.metrics[v[0]]['mids'], window.metrics[v[0]]['hist']);
                    }
                    if (v[0] == 'Site Quality') {
                        var bin = window.metrics['Site Quality']['metric'].split('_')[1];
                        $('#site_quality_note').html(get_af_bucket_text(bin));
                    }
                    draw_quality_histogram(data, '#quality_metric_container', log, v[0], 'Variants');
                    add_line_to_quality_histogram(data, v[1], '#quality_metric_container', log);
                });
            } else {
                $('#quality_metrics_container').hide();

            }
        });
    </script>
    <div class="container">
        <div class="row">
            <div class="col-md-6">
                <h1><span class="hidden-xs">Variant: </span>3:12393125 C / G</h1>
                
            </div>
            <div class="col-md-6">
            
            </div>
        </div>
        <hr/>

        
            
            <div class="row">
                <div class="col-md-6">
                    <dl class="dl-horizontal" style="margin-bottom: 0px;">
                        <dt>
                            
                                Filter Status
                            
                        </dt>
                        <dd>PASS</dd>
                        <dt>dbSNP</dt>
                        
                            <dd><a href="http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=rs1801282" target="_blank">rs1801282</a></dd>
                        
                        <dt>Allele Frequency</dt>
                        <dd>0.1101</dd>
                        <dt>Filtering AF</dt>
                        <dd data-tooltip="Filtering allele frequency (AF): a threshold for filtering variants that are too common to plausibly cause disease.
If the variant filtering AF is greater than the maximum credible population AF for the disease of interest, the variant
is too common to be causative and may be filtered. Click here to see the filtering AF calculator app and citation."><a target="_blank" href="http://cardiodb.org/allelefrequencyapp/">
                        0.1225 (Latino)</a></dd>
                        <dt>Allele Count</dt>
                        <dd>13354 / 121246</dd>
                        <dt>UCSC</dt>
                        <dd>
                            <a href="http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&highlight=hg19.chr3%3A12393125-12393125&position=chr3%3A12393100-12393150" target="_blank">
                                3-12393125-C-G
                                <i class="fa fa-external-link"></i>
                            </a>
                        </dd>
                        <dt>ClinVar</dt>
                        <dd>
                            
                                <a href="http://www.ncbi.nlm.nih.gov/clinvar?term=rs1801282%5BVariant%20ID%5D" target="_blank">
                            
                                Click to search for variant in Clinvar
                                <i class="fa fa-external-link"></i>
                            </a>
                        </dd>
                    </dl>
                </div>
                <div class="col-md-6">
                    <div class="row">
                        <div class="col-md-8 col-md-offset-1">
                            <div class="panel-group" id="metrics_outer_accordion" role="tablist" aria-multiselectable="true">
                                <div class="panel panel-default">
                                    <div class="panel-heading" role="tab" id="gt_quality_collapse_heading"   style="height: auto">
                                        <div class="panel-title">
                                            <a data-toggle="collapse" data-parent="#accordion" href="#gt_quality_collapse" aria-expanded="false" aria-controls="gt_quality_collapse">
                                                <small>Genotype Quality Metrics</small>
                                            </a>
                                        </div>
                                    </div>
                                    <div id="gt_quality_collapse" class="panel-collapse collapse" role="tabpanel" aria-labelledby="gt_quality_collapse_heading">
                                        <div class="row">
                                            <div class="col-md-10 col-md-offset-1">
                                                <div id="quality_metrics_container">
                                                    <span class="btn-group" data-toggle="buttons" id="quality_full_site_button_group">
                                                        <button class="btn btn-primary btn-sm active quality_full_site_buttons" id="variant_carriers_button"
                                                                data-tooltip="Show metric for only individuals with this allele.">
                                                            <input type="radio"> Variant carriers
                                                        </button>
                                                        <button class="btn btn-primary btn-sm quality_full_site_buttons" id="variant_site_button"
                                                                data-tooltip="Show metric for all individuals (at this site, whether or not they have this allele).">
                                                            <input type="radio" > All individuals
                                                        </button>
                                                    </span>
                                                    <div id="quality_display_container" class="d3_graph"></div>
                                                    <small><span class="label label-info">Note:</span> Plot may include low-quality genotypes that were excluded from allele counts in the table above</small>
                                                    <span class="btn-group" data-toggle="buttons" id="quality_display_button_group" >
                                                        <button class="btn btn-primary btn-sm active quality_display_buttons" id="genotype_depths_button"
                                                                data-tooltip="Per sample depth. Capped at 100X">
                                                            <input type="radio"> Depth
                                                        </button>
                                                        <button class="btn btn-primary btn-sm quality_display_buttons" id="genotype_qualities_button"
                                                                data-tooltip="Per sample genotype quality.">
                                                            <input type="radio" > Genotype Quality
                                                        </button>
                                                    </span>
                                                </div>
                                                <br/>
                                            </div>
                                        </div>
                                    </div>
                                </div>
                                <div class="panel panel-default">
                                    <div class="panel-heading" role="tab" id="quality_collapse_heading"   style="height: auto">
                                        <div class="panel-title">
                                            <a data-toggle="collapse" data-parent="#accordion" href="#quality_collapse" aria-expanded="false" aria-controls="quality_collapse">
                                                <small>Site Quality Metrics</small>
                                            </a>
                                        </div>
                                    </div>
                                    <div id="quality_collapse" class="panel-collapse collapse" role="tabpanel" aria-labelledby="quality_collapse_heading">
                                        <div class="row">
                                            <div class="col-md-10 col-md-offset-1">
                                                <div id="quality_metric_container"></div>
                                                <small><div id="site_quality_note"></div></small>
                                                <small><span class="label label-info">Note:</span> These are site-level quality metrics: they may be unpredictable for multi-allelic sites.</small>
                                                <select id="quality_metric_select" class="form-control">
                                                    <option><small>Site Quality: 23578765.28</small></option>
                                                    
                                                        <option><small>BaseQRankSum: -1.368e+00</small></option>
                                                    
                                                        <option><small>MQRankSum: 0.126</small></option>
                                                    
                                                        <option><small>InbreedingCoeff: 0.0215</small></option>
                                                    
                                                        <option><small>VQSLOD: 6.79</small></option>
                                                    
                                                        <option><small>FS: 0.000</small></option>
                                                    
                                                        <option><small>MQ: 59.67</small></option>
                                                    
                                                        <option><small>DP: 2984626</small></option>
                                                    
                                                        <option><small>QD: 13.20</small></option>
                                                    
                                                        <option><small>ClippingRankSum: -2.690e-01</small></option>
                                                    
                                                        <option><small>ReadPosRankSum: 0.336</small></option>
                                                    
                                                </select>
                                                <br/>
                                            </div>
                                        </div>
                                    </div>
                                </div>
                            </div>
                        </div>
                    </div>
                </div>
            </div>
            <hr/>
        


        <div class="row">
            <div class="col-md-6">
                <div id="annotation_container">
                
                    <div class="section_header">Annotations</div>
                    
                        <p>This variant falls on 14 transcripts in 1 genes:</p>
                        <div class="panel-group" id="annotation_accordion" style="margin-bottom: 0px;">
                            <div class="row">
                                
                                    <div class="col-md-6" style="border-right: 1px dashed #AAA;">
                                
                                
                                    <span class="h4">missense</span>
<span style='float: right;'>

</span>
<ul>
    
        <li>
            <a href="/gene/ENSG00000132170">
            
                PPARG
            
            </a>
            
                <span class="dropdown">
                    <button class="btn btn-default dropdown-toggle" type="button" id="transcript_dropdown" data-toggle="dropdown">
                        Transcripts
                        <span class="caret"></span>
                    </button>
                    <ul class="dropdown-menu" role="menu" aria-labelledby="transcript_dropdown">
                        
                            <li role="presentation">
                                <a role="menuitem" tabindex="-1" href="/transcript/ENST00000287820">
                                    ENST00000287820
                                    
                                        *
                                    
                                    
    (p.Pro12Ala)<br/>
    &nbsp; &nbsp; &nbsp; Polyphen:
    
    
    
    
    <span class=bg-success>benign</span>; SIFT:
    <span class=bg-danger>tolerated_low_confidence</span>

                                </a>
                            </li>
                        
                            <li role="presentation">
                                <a role="menuitem" tabindex="-1" href="/transcript/ENST00000397023">
                                    ENST00000397023
                                    
                                    
    (p.Pro12Ala)<br/>
    &nbsp; &nbsp; &nbsp; Polyphen:
    
    
    
    
    <span class=bg-danger>unknown</span>; SIFT:
    <span class=bg-danger>deleterious_low_confidence</span>

                                </a>
                            </li>
                        
                    </ul>
                </span>
            
        </li>
    
</ul>
                                
                                    <span class="h4">non coding transcript exon</span>
<span style='float: right;'>

</span>
<ul>
    
        <li>
            <a href="/gene/ENSG00000132170">
            
                PPARG
            
            </a>
            
                
                 - <a href="/transcript/ENST00000477039">
                    ENST00000477039
                    
                </a>
                
            
        </li>
    
</ul>
                                
                                </div>
                                <div class="col-md-6">
                                
                                    <span class="h4">intron</span>
<span style='float: right;'>

</span>
<ul>
    
        <li>
            <a href="/gene/ENSG00000132170">
            
                PPARG
            
            </a>
            
                <span class="dropdown">
                    <button class="btn btn-default dropdown-toggle" type="button" id="transcript_dropdown" data-toggle="dropdown">
                        Transcripts
                        <span class="caret"></span>
                    </button>
                    <ul class="dropdown-menu" role="menu" aria-labelledby="transcript_dropdown">
                        
                            <li role="presentation">
                                <a role="menuitem" tabindex="-1" href="/transcript/ENST00000309576">
                                    ENST00000309576
                                    
                                    
                                </a>
                            </li>
                        
                            <li role="presentation">
                                <a role="menuitem" tabindex="-1" href="/transcript/ENST00000397000">
                                    ENST00000397000
                                    
                                    
                                </a>
                            </li>
                        
                            <li role="presentation">
                                <a role="menuitem" tabindex="-1" href="/transcript/ENST00000397010">
                                    ENST00000397010
                                    
                                    
                                </a>
                            </li>
                        
                            <li role="presentation">
                                <a role="menuitem" tabindex="-1" href="/transcript/ENST00000397012">
                                    ENST00000397012
                                    
                                    
                                </a>
                            </li>
                        
                            <li role="presentation">
                                <a role="menuitem" tabindex="-1" href="/transcript/ENST00000397015">
                                    ENST00000397015
                                    
                                    
                                </a>
                            </li>
                        
                            <li role="presentation">
                                <a role="menuitem" tabindex="-1" href="/transcript/ENST00000397026">
                                    ENST00000397026
                                    
                                    
                                </a>
                            </li>
                        
                            <li role="presentation">
                                <a role="menuitem" tabindex="-1" href="/transcript/ENST00000397029">
                                    ENST00000397029
                                    
                                    
                                </a>
                            </li>
                        
                            <li role="presentation">
                                <a role="menuitem" tabindex="-1" href="/transcript/ENST00000438682">
                                    ENST00000438682
                                    
                                    
                                </a>
                            </li>
                        
                            <li role="presentation">
                                <a role="menuitem" tabindex="-1" href="/transcript/ENST00000455517">
                                    ENST00000455517
                                    
                                    
                                </a>
                            </li>
                        
                            <li role="presentation">
                                <a role="menuitem" tabindex="-1" href="/transcript/ENST00000497594">
                                    ENST00000497594
                                    
                                    
                                </a>
                            </li>
                        
                            <li role="presentation">
                                <a role="menuitem" tabindex="-1" href="/transcript/ENST00000539812">
                                    ENST00000539812
                                    
                                    
                                </a>
                            </li>
                        
                    </ul>
                </span>
            
        </li>
    
</ul>
                                
                                </div>
                            </div>
                        </div>
                        <small><span class="label label-info">Note:</span> This list may not include additional transcripts in the same gene that the variant does not overlap.</small>
                    
                
                </div>
                <div id="browser_container">
                </div>
            </div>

            <div class="col-md-6">
                
                    <div id="frequency_info_container">
                        <div class="section_header">Population Frequencies</div>
                        <div id="frequency_table_container" class="frequency_displays">
                            
                            <table id="frequency_table">
                                <thead>
                                    <tr>
                                        <th>Population</th>
                                        <th>Allele Count</th>
                                        <th>Allele Number</th>
                                        
                                            <th>Number of Homozygotes</th>
                                        
                                        
                                        <th>Allele Frequency</th>
                                    </tr>
                                </thead>
                                <tbody>
                                    
                                        <tr>
                                            <td>European (Non-Finnish)</td>
                                            <td>8148</td>
                                            <td>66694</td>
                                            
                                                <td>525</td>
                                            
                                            
                                            
                                                <td>0.1222</td>
                                            
                                        </tr>
                                    
                                        <tr>
                                            <td>East Asian</td>
                                            <td>372</td>
                                            <td>8598</td>
                                            
                                                <td>5</td>
                                            
                                            
                                            
                                                <td>0.04327</td>
                                            
                                        </tr>
                                    
                                        <tr>
                                            <td>Other</td>
                                            <td>94</td>
                                            <td>908</td>
                                            
                                                <td>5</td>
                                            
                                            
                                            
                                                <td>0.1035</td>
                                            
                                        </tr>
                                    
                                        <tr>
                                            <td>African</td>
                                            <td>204</td>
                                            <td>10404</td>
                                            
                                                <td>1</td>
                                            
                                            
                                            
                                                <td>0.01961</td>
                                            
                                        </tr>
                                    
                                        <tr>
                                            <td>Latino</td>
                                            <td>1475</td>
                                            <td>11528</td>
                                            
                                                <td>88</td>
                                            
                                            
                                            
                                                <td>0.1279</td>
                                            
                                        </tr>
                                    
                                        <tr>
                                            <td>South Asian</td>
                                            <td>1979</td>
                                            <td>16504</td>
                                            
                                                <td>143</td>
                                            
                                            
                                            
                                                <td>0.1199</td>
                                            
                                        </tr>
                                    
                                        <tr>
                                            <td>European (Finnish)</td>
                                            <td>1082</td>
                                            <td>6610</td>
                                            
                                                <td>87</td>
                                            
                                            
                                            
                                                <td>0.1637</td>
                                            
                                        </tr>
                                    
                                </tbody>
                                <tfoot>
                                    <tr>
                                        <td><b>Total</b></td>
                                        <td><b>13354</b></td>
                                        <td><b>121246</b></td>
                                        
                                            <td><b>854</b></td>
                                        
                                        
                                        <td><b>
                                            
                                                0.1101
                                            
                                        </b></td>
                                    </tr>
                                </tfoot>
                            </table>
                            
                        </div>
                    </div>
                
            </div>
        </div>

        

            <hr/>

            <div class="row">
                <div class="col-md-12">
                    <div class="section_header">Read Data</div>
                    <p/>
                    
                    This interactive <a href="https://github.com/igvteam/igv.js">IGV.js</a> visualization shows reads
                    that went into calling this variant.<br>
                    <small><span class="label label-info">Note:</span> These are reassembled reads produced by
                        <a href="https://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_gatk_tools_walkers_haplotypecaller_HaplotypeCaller.php#--bamOutput">
                            GATK HaplotypeCaller --bamOutput
                        </a> so they accurately represent what HaplotypeCaller was seeing when it called this variant.
                    </small>
                    <br><br>

                    <div id="igv-container"></div>
                    <br><br>

                    
                    <center>
                        <button class="btn btn-primary quality_full_site_buttons"
                                style="disabled:true; width:130px; height: 32px;" id="load-more-het-button">Load +1 Het
                        </button>
                        &nbsp; &nbsp; &nbsp;
                        <button class="btn btn-primary quality_full_site_buttons"
                                style="disabled:true; width:130px; height: 32px;" id="load-more-hom-button">Load +1 Hom
                        </button>
			
                        <br>
                    </center>
                    
                    <br>

                    <!-- IGV dependencies -->

                    <!-- igv.js -->
                    <!-- link rel="stylesheet" type="text/css" href="/igv-css/igv.css" -->
                    <!-- script type="text/javascript" src="/igv.min.js"></script -->

                    <link rel=stylesheet type=text/css href="/static/css/igv.css">
                    <script type="text/javascript" src="/static/igv.min.js"></script>

                    <!-- link rel="stylesheet" type="text/css" href="http://igv.org/web/beta/igv-beta.css" -->
                    <!-- script type="text/javascript" src="http://igv.org/web/beta/igv-beta.min.js"></script -->

                    <script type="text/javascript">

                        var get_bam_track_config = function (read_viz_data, het_or_hom_or_hemi, i) {
                            return {
                                type: 'bam',
                                indexed: true,
                                alignmentShading: 'strand',
                                url: '/read_viz/' + read_viz_data[het_or_hom_or_hemi]['urls'][i],
                                name: het_or_hom_or_hemi + ' #' + (i + 1),
                                height: 300,
                                minHeight: 300,
                                autoHeight: false,
                                readgroup: read_viz_data[het_or_hom_or_hemi]['readgroups'][i],  //readgroup: '1-157768000-G-C_hom10',
                            };
                        };

                        // global igv settings
                        igv.CoverageMap.threshold = 0.1;

                        // temporary implementation of filtering IGV BamTracks by a user-specified ReadGroup
                        igv.BamReader.prototype.readFeatures_original = igv.BamReader.prototype.readFeatures;
                        igv.BamReader.prototype.readFeatures = function (chr, min, max, continuation, task) {

                            //if a readgroup was passed to the BamTrack constructor, filter reads without this read group.
                            if (this.config.readgroup) {
                                var readgroup = this.config.readgroup;
                                var continuation_original = continuation;
                                var continuationNew = function (alignments) {
                                    //filter the alignments by read group
                                    //console.log("Filtering by RG == " + readgroup );
                                    alignments = alignments.filter(function (alignment) {
                                        alignment.tags(); //parses tags from their binary representation and populates the alignment.tagDict
                                        return alignment.tagDict['RG'] == readgroup;
                                    });

                                    //forward the filtered aligments to the original continuation
                                    return continuation_original(alignments);
                                };
                            }

                            return this.readFeatures_original(chr, min, max, continuationNew, task);
                        };

                        //a dict of counts: n_expected_het, n_expected_hom, n_available_het, n_available_hom
                        var read_viz_data = {"hemi": {"n_available": 0, "n_expected": 0, "readgroups": [], "urls": []}, "het": {"n_available": 5, "n_expected": 5, "readgroups": ["3-12393125-C-G_het0", "3-12393125-C-G_het1", "3-12393125-C-G_het2", "3-12393125-C-G_het3", "3-12393125-C-G_het4"], "urls": ["combined_bams_v3/3/combined_chr3_125.bam", "combined_bams_v3/3/combined_chr3_125.bam", "combined_bams_v3/3/combined_chr3_125.bam", "combined_bams_v3/3/combined_chr3_125.bam", "combined_bams_v3/3/combined_chr3_125.bam"]}, "hom": {"n_available": 5, "n_expected": 5, "readgroups": ["3-12393125-C-G_hom0", "3-12393125-C-G_hom1", "3-12393125-C-G_hom2", "3-12393125-C-G_hom3", "3-12393125-C-G_hom4"], "urls": ["combined_bams_v3/3/combined_chr3_125.bam", "combined_bams_v3/3/combined_chr3_125.bam", "combined_bams_v3/3/combined_chr3_125.bam", "combined_bams_v3/3/combined_chr3_125.bam", "combined_bams_v3/3/combined_chr3_125.bam"]}, "total_available": 10, "total_expected": 10};

                        //counts number of het/hom bam tracks displayed so far
                        var tracks_counter = {"het": 0, "hom": 0, "hemi": 0};

                        //initialize IGV tracks
                        var tracks = [];
                        tracks.push({
                            url: '/read_viz/gencode.v19.sorted.bed',
                            name: "gencode v19",
                            displayMode: "SQUISHED"
                        });
                        //tracks.push({ url: '/read_viz/exome_calling_regions.v1.bed', name: "ExAC calling regions" });
                        //tracks.push({ url: '/read_viz/self_chain.sorted.bed',        name: "UCSC self chain" });

                        if (location.hash == '#all') {
                            //add all available tracks for het and hom and hide the 'load +1' buttons
                            // this mode was requested by Konrad and Eric
                            ["het", "hom", "hemi"].forEach(function (het_or_hom_or_hemi) {
                                $('#load-more-'+het_or_hom_or_hemi+'-button').hide();
                                var n = read_viz_data[het_or_hom_or_hemi]['n_available'];
                                for (var i = 0; i < n; i += 1) {
                                    tracks.push(get_bam_track_config(read_viz_data, het_or_hom_or_hemi, i));
                                    tracks_counter[het_or_hom_or_hemi] += 1;
                                }
                            });

                        } else {
                            //add track #1 for het and hom (assuming they're available)
                            ["het", "hom", "hemi"].forEach(function (het_or_hom_or_hemi) {
                                if (read_viz_data[het_or_hom_or_hemi]['n_available'] > 0) {
                                    tracks.push(get_bam_track_config(read_viz_data, het_or_hom_or_hemi, 0));
                                    tracks_counter[het_or_hom_or_hemi] += 1;
                                }

                                disable_load_one_more = tracks_counter[het_or_hom_or_hemi] >= read_viz_data[het_or_hom_or_hemi]['n_available'];
                                $('#load-more-' + het_or_hom_or_hemi + '-button').prop('disabled', disable_load_one_more);
                            });

                            var load_one_more = function (het_or_hom_or_hemi) {
                                if (tracks_counter[het_or_hom_or_hemi] < read_viz_data[het_or_hom_or_hemi]['n_available']) {
                                    var i = tracks_counter[het_or_hom_or_hemi];
                                    console.log(read_viz_data[het_or_hom_or_hemi]['urls'][i]);
                                    console.log(read_viz_data[het_or_hom_or_hemi]['readgroups'][i]);
                                    igv.browser.loadTrack(get_bam_track_config(read_viz_data, het_or_hom_or_hemi, i));
                                    tracks_counter[het_or_hom_or_hemi] += 1;
                                }

                                if (tracks_counter[het_or_hom_or_hemi] >= read_viz_data[het_or_hom_or_hemi]['n_available']) {
                                    $('#load-more-'+het_or_hom_or_hemi+'-button').prop('disabled', true);
                                }
                            };

                            $('#load-more-het-button').click(function () {
                                load_one_more("het");
                            });

                            $('#load-more-hom-button').click(function () {
                                load_one_more("hom");
                            });

                            $('#load-more-hemi-button').click(function () {
                                load_one_more("hemi");
                            });
                        }



                        //initialize IGV.js browser
                        var locus = '3:12393085-12393165';
                        var options = {
                            showCommandBar: true,
                            genome: 'hg19',
                            locus: locus,
                            showKaryo: false,
                            tracks: tracks,
                        };

                        igv.createBrowser($("#igv-container")[0], options);


                        //IGV browser customizations
                        $(".igv-ideogram-content-div").hide();  //hide the IGV ideogram

                        //$(".igv-logo").hide();

                        $(".igvNavigationSearch").append(
                                "<a id='reset-locus' title='Reset to original locus (" + locus + ")'>" +
                                "<i class='igv-app-icon fa fa-mail-reply shim-left-6'></i>" +
                                "</a>");

                        // allow one more zoom-in level
                        igv.browser.pixelPerBasepairThreshold = function () {
                            return 28.0;  //default is currently 14.0
                        };

                        //click handlers
                        $('#reset-locus').click(function () {
                            igv.browser.search(locus);
                        });

                        igv.browser.trackViews.forEach(function (panel) {
                            if (panel.track.name) {
                                //add border between tracks
                                panel.viewportDiv.style.borderBottom = panel.viewportDiv.style.borderLeft = "1px solid #cccccc";
                            }
                        });

                    </script>
                    <style>
                        .igv-viewport-div {
                            border-left: 1px solid #cccccc;
                            border-bottom: 1px solid #cccccc;
                        }
                    </style>
                    
                </div>
            </div>
	    
        </div>



</body>